#12 · Tools & infrastructure
New tools for recombination, metagenomic decontamination, and microbial community design
The dominant thread is packaging microbial sequence and community analysis methods as installable, reusable tools. Verticall detects recombinant regions in bacterial genome assemblies and builds recombination-free phylogenies at scale. Metacontam performs control-free, species-level decontamination of shotgun metagenomes, and MetaMAG Explorer recovers and dereplicates MAGs while augmenting Kraken2 databases for classification. MycorrhizaTracer automates BLAST-based taxonomic classification of Sanger chromatograms. LEMMIv2 extends this logic to evaluation through continuous benchmarking of metagenomic and 16S amplicon profilers, and SynCom101 to in silico design of synthetic microbial communities. The set is heterogeneous, so not every item shares this thread. What is new is the breadth of functions, from recombination detection to community design, now available within one tool class.
Preprints
Prioritizing peptides for targeted mass spectrometry experiments using deep learning
Bromo, a transformer model that ranks peptide precursors by relative MS response with charge state, outperforms sequence-based methods and can be fine-tuned…
maxiM/Ze: An Image Recognition Approach for Visualizing and Processing Mass Spectrometry Based Metabolomics Data
maxiM/Ze is a Python tool that applies OpenCV image recognition to LC-HRMS EICs for automated metabolomics peak alignment, validated against Compound…
TIMS-Bench: Towards community standards for benchmarking untargeted trapped ion mobility metabolomics tools and datasets
Benchmarks three TIMS feature-finding tools (MZmine, MS-DIAL, MetaboScape) on ten public and three benchmark datasets, releasing ground-truth data and code.
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